In developing Acuity® 4.0 we have concentrated on cross-platform support, data warehousing,
and new enabling analysis and visualization tools:
Cross-platform functionality
Acuity now supports Oracle as well Microsoft SQL Server databases.
Robust Multichip Analysis (RMA) using quantile or cyclic loess normalization, and summarization by robust linear models or median polish.
Data warehousing
Store all files types in the Acuity database, attached to microarrays or datasets: TIFF, GPS, GAL, PDF, HTM, BMP, JPEG, etc.
Save web pages to the database.
Annotation warehouses to manage annotations by user or by genome.
Many database management tools, such as database backup and restore, apply GAL files to microarrays, and merge microarrays.
Analyses and visualizations
Multiclass classification and variable selection for finding genes that discriminate among classes of microarrays.
Chromosome visualization to plot expression data directly on chromosome maps.
Fully configurable scatter plots of any data columns, including results of t-tests (volcano plots), ANOVA and principal components analysis.
User-definable profiles to find matching expression profiles.
Arbitrary gene list unions and intersections.
Expanded scripting model.
Click on thumbnails below
A volcano plot is a scatter plot of -log (p-value) from a t-test or one-way ANOVA, versus log ratio. It allows you to
visualize fold-change and statistical significance at the same time, so that one can find genes that are significant and
have large fold change, or genes that are significant but have small fold change.
Plot expression or CGH data directly on fully interactive chromosome maps of your genome. The top view shows a
high-level view of expression data across all chromosomes, while the bottom view is a zoomed view of an area of interest.
Use the profile editor to define expression profiles to search for in your data.
Acuity's Normalization Wizard can normalize an arbitrary number of microarrays with the click of a button.
Choose to normalize on all spots, control spots, negative controls or any other subset of spots that you can
specify with a fully general database query. Normalize groups of microarrays to a time point or a sample.
Choose linear ratio-based methods or non-linear lowess methods, including print-tip groups. Normalizations
are easy to apply and remove so that you can experiment freely with different methods. Once you are finished,
unnormalized and normalized data are displayed side-by-side in the Normalization Viewer.
Filtering
Establishing data quality is paramount in microarray experiments, as unbiological outliers can skew downstream
analyses. Acuity has a large number of analytical and statistical tools that you can use to filter out noise
from your data: filter on replicate statistics, on individual spot characteristics or on many other quality measures.
Once you have identified outliers, update their flag values in the database, or define your own custom flag values.
Tracking replicate substances and microarrays is intrinsic to Acuity analyses. Replicate substances are automatically
combined, and can be filtered by standard deviation, coefficient of variation and many other measures. Replicate
microarrays can be easily combined to construct representative data points from each time or for each tissue in an
experiment.
Find Matching Expression
Use Acuity's Match Expression function to investigate the behaviour of individual substances in your experiment.
Choose from nine different similarity metrics to find the substances that are most highly correlated with a single
profile or to an average profile built from a class of substances.
There is no single analysis technique that can be used for all types of data, so Acuity has a suite of advanced
analysis methods, among them Hierarchical Clustering, Self-Organizing Maps, K-Means and K-Medians, Gap Statistic,
Principal Components Analysis, Gene Shaving and more. Each algorithm offers a large choice of similarity metrics,
so that you can use the analysis that is appropriate for your data.
Use the output of one algorithm as input to the next. For example, you can optimally order the branches in a
dendrogram from a hierarchical cluster, with the order derived from a Self-Organizing Map or a Principal
Components Analysis.
Performance Optimization
All Acuity analyses have been optimized for speed and memory use on very large data sets so that a standard desktop
computer can be used to cluster hundreds of microarrays. Clustering and other processor-intensive tasks are implemented
as background processes, so that you can queue and execute multiple analysis tasks while continuing to work on other
tasks in Acuity. Depending on the size of the dataset and the amount of computer memory available to Acuity, the
clustering algorithms partition the datasets and perform calculations differently, so that Acuity is always working
most efficiently.
Analysis Audit Trail
All Acuity analysis operations and results are stored sequentially in the database as they are calculated, so an
audit trail is maintained automatically and displayed in the Acuity project tree for each data set. You can easily
reproduce an analysis, or remove data transformations from microarrays or datasets.
Acuity Quicklists are a powerful method of saving lists of interesting substances, microarrays or annotations.
With the click of the mouse you can save all selected substances as a quicklist, either globally or with a dataset.
Each list can be assigned a color. Together with the ability to apply a list to the current view of the data, so
that the substances and microarrays are colored appropriately, colored quicklists give you the ability to track
multiple sets of substances through all Acuity visualizations.
Reports and Scripting
Like GenePix Pro, Acuity supports standard scripting languages such as VBScript and JavaScript, as well as any
other scripting languages supported by Internet Explorer, such as PerlScript and PythonScript. Extract data via
script, write custom analyses through ActiveX objects, generate HTML reports: Acuity scripting is maximally flexible.
Visualizations
Clear and Interactive
Acuity's clear and interactive display of analyzed data can reveal subtle structure and relationships in the data
that are not apparent from less elegant visualizations. Acuity displays clustering results in many different ways,
uses smooth interactive 3-D plots of principal components data (exportable as AVI animations), and synchronizes all
views so that substances and their annotations selected in one view are automatically grouped in all other views.
Color Tables
The Color Table is the central data view in Acuity. Microarrays are organized into columns, with substances in rows.
The table is colored automatically based on user-specified thresholds, and these colors are propagated throughout Acuity.
Expression Profiles
Clusters and other color-based visualizations do not always demonstrate the co-expression of a set of substances as
effectively as a simple line plot. Examine the expression profiles of groups of substances easily with the Acuity
Graph tab.
3D Scatter Plots
Some analyses, such as Principal Components Analysis, are best displayed in three dimensions. Acuity's 3D display
is fast, smooth and fully interactive, so that you can easily rotate, zoom and select points of interest. You can
also export rotating animations as AVI for display on web sites.
Microarray and Substance Summaries
Display dataset, microarray or substance summaries at any time.
Single Microarray View
You always have access to your original raw data in Acuity, including GenePix analysis images. View your raw data
at any time, linked to images, and draw scatter plots of raw data columns. This is an essential tool for microarray
quality control.
Web Links
With Acuity's web links functionality you are only ever a click away from looking up a substance in any web-based
database. Define as many web links as you like, and look up substances based on any identifier.
Pathways
Link directly to web-based pathway sites such as KEGG or BioCarta and display and interact with them in the
Acuity interface.
Save As PDF
Easily generate publication-quality graphics in Portable Document Format (PDF) from all your Acuity analysis
visualizations. PDF files are compact enough to send as email attachments but retain layout and font information,
as well as preserving the resolution and quality of graphs and images. PDF files are text searchable and seamlessly
import into publishing software packages such as Adobe Photoshop or Illustrator as vector graphics, so that they can
be resized without loss of quality.
Data Management
A Scaleable Relational Database
Data management is the essence of bioinformatics: it is pointless having good data if you cannot store it, access it
and share it with colleagues and collaborators. Central to Acuity is its powerful and scaleable relational database
that can effortlessly store and retrieve terabytes of data. Acuity users can connect to a central Acuity server
from home, from another lab or from the other side of the world. All configurations are as simple as double-clicking
on the Acuity icon.
Acuity now has additional tools for managing multiple users at the enterprise level: set permissions for users and
groups on a folder-by-folder basis, show and hide folders from users and groups. Enterprise microarray informatics
has never been easier or more affordable.
Full Integration with GenePix Pro
GenePix scanners,
GenePix Pro and Acuity form a single, integrated system.
Perform acquisition, first-pass analysis and advanced analysis all within the one environment. Save your data
directly from GenePix Pro to the Acuity database with the GenePix Pro "Save To Acuity" command. At the enterprise
level, use the Acuity database as a centralized repository for GenePix data.
Acuity imports normalized GenePix Pro files in their normalized state, so that they can be unnormalized or
renormalized in Acuity using the same normalization method that was used in GenePix Pro. Acuity recognizes
GenePix Pro flagged features, so that when you select features on the image in the Acuity Results tab, the
GenePix flags are displayed (see below).
Familiar Interface
The Acuity Project Tree is a high-level view of the Acuity database. Import thousands of microarrays and organize
them with a Windows Explorer-like tree.
The Tree behaves like any other Windows tree. You can cut, copy, paste, drag and drop, rename and delete microarrays,
folders, datasets and quicklists in the familiar way, as well as assigning access and permissions to users.
Full Database Queries
Construct datasets with fully general queries across the entire database with the Query Wizard. The Query Wizard
allows you to build complex database queries by combining a series of simple, step-by-step conditions.
Scatter plots from the Acuity Normalization Viewer showing unnormalized and lowess normalized data for one microarray,
with print-tip smoothing curves.
Store microarray parameters, such as clinical information, in the Acuity database, and browse the data at any time.
A graph of the Gap statistic for a dataset, showing that four clusters is the best partition of the data.
Each dataset is stored in the database together with all the transformations and analyses performed on the data,
maintaining an analysis audit trail.
Construct ontologies from substance annotations, such as this one of molecular functions in yeast.
Statistics calculated on replicate substances and microarrays can be viewed next to your data at any time.
Annotation data imported to the Acuity database can be viewed next to your data at any time.
Hyperlinks to an unlimited number of online databases can be viewed next to your data at any time, and the web pages
displayed inside the Acuity interface.
A 3D scatter plot exported from Acuity showing samples from various cancer cell lines separated in the principal
components space. [AVI] (1.4 MB)
Select features on imported analysis images using the lasso tool in Acuity. Update flags in the database, or define
your own custom flag values, based on selections on the image.
A dendrogram of a time course experiment. Note the neat separation of the data into up- and down-regulated substances.
All Acuity visualizations are exportable in PDF format. [PDF] (360 KB)
A self-organizing map of four replicate arrays, where the second two are dye swaps of the first two: note on the
top left and bottom right the clusters containing highly differentially expressed substances with good replication
across the four arrays.
Activity profiles of the two clusters of interest from the replicate dye swap experiment described above. This is
a useful diagnostic: note that the first microarray has a larger dynamic range than the next three.
Use the scatter plot as another method of examining the distribution of your data, for any data type.
Inspect a summary of all information in the database about any substance or microarray, at any time.
Export microarrays in MAGE-ML format for upload to web-based databases such as ArrayExpress. A growing number
of journals, such as Nature, are requiring that microarray data is made available in MAGE-ML format as part of
publication. Acuity gives you the ability to export data in this format. Acuity has on-the-fly compression during
export to minimize file sizes.
Track Microarrays
Manage all the properties of your microarrays, from slide production through scanning and analysis, and store them
in the database, where they can be searched or used to filter data. Acuity can be an indispensable part of your
laboratory information management system, as all your microarray experimental data is recorded, stored, analyzed
and displayed in the one place.
Annotation Management
The Acuity database manages annotations automatically. Once annotations are imported, they are displayed whenever
a substance is displayed. You can annotate substances using an unlimited number of properties, and link directly
to an unlimited number of web-accessible databases. Acuity includes a tool to build standard ontologies (biological
process, cellular component, molecular function) automatically from your annotations.
Universal Text File Import
Acuity imports tab-delimited text files from any source. Import microarray data
files, experiment descriptions, substance annotations or any other data in tab-delimited files.
Advanced Database Management Tools
As well as tools to manage users, groups and permissions, Acuity has advanced tools to manage your database at
a very low level. Add and delete fields, re-build table indexes to optimise database performance, and create new
ODBC connections all from the Acuity client.
Easy To Use
Acuity makes enterprise microarray informatics accessible to everyone. From installing and maintaining the database,
to managing users and groups through to filtering and analyzing your data, Axon has put every effort into giving
Acuity an intuitive interface. Common tasks are all accessible through small wizards on a toolbar, so that novices
can get started on real work quickly.
Optimized for Windows
Microarray datasets are large, and are only going to get larger. Because Acuity has been designed and optimized
for Windows, it effortlessly manages large datasets, many simultaneous users, and multiple concurrent analyses and
visualizations. There are no bottlenecks to accessing, searching, filtering or analyzing your data. If you work
on Windows platforms, it makes sense to use software that has been designed and optimized for Windows.
No License Fees
Buy Acuity once and use it forever. Unlike other array informatics software, there are no recurring license fees,
you are never locked out of your data, and you can download all minor version upgrades for free.
Acuity Feature List
Analysis
Hierarchical clustering with many different similarity metrics.
Self-organizing maps (SOMs) with many different similarity metrics.
Order dendrograms with SOMs, PCA.
K-Means and K-Medians with many different similarity metrics.
Gap Statistic to estimate optimal number of K-Means and K-Medians clusters.
Principal components analysis.
Gene Shaving.
Find similar expression profile with the following similarity metrics.
Find similar expression profile to user-defined profile.
Variable selection with diagonal linear and quadratic discriminant analysis.
Robust Multichip analysis (RMA).
Import and display full annotation data in an unlimited number of columns.
Import and export gene lists.
Import and export datasets.
Import chromosome data.
Substance lists and associated colors.
Union and intersection of lists.
Normalization wizard, including ratio-based normalization, wavelength-based normalization, print-tip lowess normalization with options for centering and scaling data, normalization to time points and samples.
Statistics calculated for replicate microarrays, including mean, median, coefficient of variation, standard deviation, maximum, minimum.
Significance statistics (p-values) calculated by Two-Sample Student's t-Test or Mann-Whitney test, and corrections for multiple hypothesis testing by Bonferroni, Step-Down Bonferroni, Hochberg, Sidak, Step-Down Sidak, and Benjamini-Hochberg methods.
Multiple group comparisons by one-way ANOVA.
Support for dye-swap microarrays in datasets.
Column arithmetic on any data column.
Multiple column transformations on datasets (row and column centering and scaling).
Image display and integration with data tables, scatter plots and all other visualizations in Acuity.
Lasso selection on images.
User-definable flag values.
Scripting engine for customizable analysis through VBScript, JavaScript or ActiveX objects.
Analysis queuing.
Fully integrated with GenePix Pro.
Web links for unlimited access to web-based databases, including pathways.
Create datasets from completely general database queries across all microarrays and all annotations in the database.
Construct ontologies from imported gene ontology information.
Merge microarrays.
Apply GAL file to microarrays.
Visualizations
Dendrograms.
2-D interactive plots.
Animated interactive 3-D scatter plots.
Chromosome visualization.
Normalization Viewer shows unnormalized and normalized data in the same window in scatter plots or histograms.
M v A plots, including lowess print-tip smoothing curves.
Line graphs of any microarray parameter.
Scatter plots of any GPR or other microarray data type, or any analysis data type, such as p-value or correlation coefficient.
Color tables.
Export any visualization as PDF, BMP or WMF.
Export animated 3D scatter plots as AVI.
Database
Support for Microsoft SQL Server 2000, Oracle 9ir2, and Oracle 10gr1.
ODBC-compliant.
Full client-server model for effortless local, LAN or remote TCP/IP access.
Tools for creating and managing users and groups.
Users with read only, read-write or lab head permissions.
Advanced database search tools.
Advanced database management tools, such as a database optimizer to re-build database table indices.
Organize substance annotations into warehouses and genomes.
True copy and paste of microarrays in the database.
Attach (import) any file type to a microarray or a dataset in the database.
Database backup and restore utility (SQL Server only).
Database Recycle Bin to permanently delete or restore deleted data.
Compact database tool to minimize database size on disk.
Universal text file import, including GenePix Pro GPR files.
Includes Microsoft SQL Server 2000 Desktop Edition.
Computer Requirements
Acuity is fully functional with the Minimum computer requirements. Server performance, particularly with
multiple users, affects the speed with which you can access your data, while client performance affects the
speed with which you can analyze (e.g., cluster) your data. Computer workstations purchased from Molecular
Devices will meet or exceed the Recommended Client configuration.
Note: The same computer can be a client and a server, so for a single seat license you
can run Acuity on one computer only.
Minimum Client or Server
IBM-compatible computer with a 1 GHz Pentium (32-bit) or faster
Windows 98 or ME operating system (dual-boot systems are not recommended)
256 MB RAM
Hard disk with 10 GB free
CD-ROM for installation
1024 x 768 display system with 65K colors
Internet Explorer 6.0 or higher
USB port
Recommended Client
IBM-compatible computer with a 2 GHz Pentium (32-bit) or faster
Windows 2000 or XP operating system (dual-boot systems are not recommended)
768 MB RAM or more
Hard disk with 30 GB free
Recordable/Rewriteable CD-ROM
1280 x 1024 display system with 16M colors
Internet Explorer 5.0 or higher
100 Base-T network card
Internet access (for faster version updates and troubleshooting)
Recommended Server
Please discuss your server requirements with your computer vendor. Server specifications depend strongly on the
number of simultaneous users to support. We recommend the following:
Windows 2000 Server operating system
768 MB RAM or more
Back-up device for data backup
USB port for software security key (dongle)
Acuity on a Mac
The Acuity client is fully compatible with Virtual PC 6 running on Macintosh OS X 10.2.
We have tested the following minimum configuration:
Mac OS 10.2
1 GHz G4 iMac
256 MB RAM
Virtual PC 6.0 running Windows 2000 with 160 MB dedicated to it
The Acuity SQL Server database and network security key should be installed on a Windows computer.
Acuity Demonstration
Use the Literature link in the right menu to download a fully-functional time-limited demonstration copy
of the Acuity software.
MSDE is a version of SQL Server 2000 suitable for single-user desktop operation, for databases up to 2 GB. For
multi-user Acuity installations or for databases larger than 2 GB, customers must purchase Microsoft SQL Server
2000 separately.
